+Open data
-Basic information
Entry | Database: PDB / ID: 1p8t | |||||||||
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Title | Crystal structure of Nogo-66 Receptor | |||||||||
Components | Reticulon 4 receptor | |||||||||
Keywords | SIGNALING PROTEIN / NgR / Nogo-66 | |||||||||
Function / homology | Function and homology information neuronal signal transduction / ganglioside GM1 binding / chondroitin sulfate binding / neuregulin receptor activity / ganglioside GT1b binding / negative regulation of axon regeneration / negative regulation of axon extension / Axonal growth inhibition (RHOA activation) / corpus callosum development / positive regulation of Rho protein signal transduction ...neuronal signal transduction / ganglioside GM1 binding / chondroitin sulfate binding / neuregulin receptor activity / ganglioside GT1b binding / negative regulation of axon regeneration / negative regulation of axon extension / Axonal growth inhibition (RHOA activation) / corpus callosum development / positive regulation of Rho protein signal transduction / axonal growth cone / axonogenesis / positive regulation of GTPase activity / dendritic shaft / presynapse / negative regulation of neuron projection development / signaling receptor activity / heparin binding / perikaryon / cell surface receptor signaling pathway / neuron projection / membrane raft / external side of plasma membrane / neuronal cell body / glutamatergic synapse / protein-containing complex binding / cell surface / endoplasmic reticulum / extracellular exosome / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å | |||||||||
Authors | Barton, W.A. / Liu, B.P. / Tzvetkova, D. / Jeffrey, P.D. / Fournier, A.E. / Sah, D. / Cate, R. / Strittmatter, S.M. / Nikolov, D.B. | |||||||||
Citation | Journal: Embo J. / Year: 2003 Title: Structure and axon outgrowth inhibitor binding of the Nogo-66 receptor and related proteins Authors: Barton, W.A. / Liu, B.P. / Tzvetkova, D. / Jeffrey, P.D. / Fournier, A.E. / Sah, D. / Cate, R. / Strittmatter, S.M. / Nikolov, D.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p8t.cif.gz | 63 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p8t.ent.gz | 50.2 KB | Display | PDB format |
PDBx/mmJSON format | 1p8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p8t_validation.pdf.gz | 408.4 KB | Display | wwPDB validaton report |
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Full document | 1p8t_full_validation.pdf.gz | 421.3 KB | Display | |
Data in XML | 1p8t_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 1p8t_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/1p8t ftp://data.pdbj.org/pub/pdb/validation_reports/p8/1p8t | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31615.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: 293 Cells / References: UniProt: Q9BZR6 |
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#2: Sugar | ChemComp-NAG / |
#3: Sugar | ChemComp-NDG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 1.21 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.21 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→35 Å / Num. obs: 34022 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection | *PLUS Redundancy: 4.4 % / Rmerge(I) obs: 0.071 |
Reflection shell | *PLUS % possible obs: 99 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.2→20 Å
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Refinement | *PLUS Lowest resolution: 8 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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